PatternLab for Proteomics

PatternLab for Proteomics is an integrated computational environment for analyzing shotgun proteomic data. PatternLab contains modules for formatting sequence databases, performing peptide spectrum matching, statistically filtering and organizing shotgun proteomic data, extracting quantitative information from label-free and chemically labeled data, performing statistics for differential proteomics, displaying results in a variety of graphical formats, performing similarity-driven studies with de novo sequencing data, analyzing time-course experiments, and helping with the understanding of the biological significance of data in the light of the Gene Ontology. Here we present PatternLab for Proteomics 4.0, which closely knits together all these modules in a self-contained environment, covering the principal aspects of proteomic data analysis as freely available and easily installable software.

PatternLab is user-friendly, simple and provides a graphical user interface.

When using PatternLab please cite:

DOI of the manuscript

Paulo C Carvalho, Diogo B Lima, Felipe V Leprevost, Marlon D M Santos, Juliana S G Fischer, Priscila F Aquino, James J Moresco, John R Yates III, Valmir C Barbosa, “Integrated analysis of shotgun proteomic data with PatternLab for proteomics 4.0”,
Nature Protocols (11), 102-117 (2016)

Publications in peer reviewed journals:

  1. "PatternLab for proteomics: a tool for differential shotgun proteomics.", BMC bioinformatics, v. 9, p. 316, 2008.
  2. "Analyzing shotgun proteomic data with PatternLab for proteomics.", Current Protocols in Bioinformatics, v. Chapter 13, p. Unit 13.13, 2010.
  3. "PatternLab: from mass spectra to label-free differential shotgun proteomics.", Current Protocols in Bioinformatics , v. Chapter 13, p. Unit 13.19, 2012.

External Patternlab's Modules

Spectrum Identification Machine for Cross-linked peptides (SIM-XL)

⇒ A search engine tool that can analyze data generated through commonly used cross-linkers (e.g., BS3/DSS). SIM-XL introduces a new paradigm for search-space reduction, which ultimately accounts for its increase in speed and sensitivity. SIM-XL is the first tool to support XL data in the mzIdentML format.


⇒ A software tool that can deisotope and decharge high-resolution mass spectra from large peptide molecules, link the precursor monoisotopic peak information to the corresponding tandem mass spectrum, and account for different co-fragmenting ion species (multiplexed spectra).

Recommended Software

Rapid novor - Speed up discovery

De novo sequencing is the method of choice for analyzing mass spectrometry based proteomics data of unsequenced organisms. Rapid Novor is a freely available for academic use de novo sequencing tool that has shown to excel over widely adopted tools. Rapid Novor is supported through PatternLab's PepExplorer module to enable similarity-driven studies helping put together the various sequenced peptides into a protein report with a FDR to satisfy the classical proteomic standards.